Hi Javier - the RMSDs are reported as attributes, so you could just write them to a file. take a look at https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes Hope that helps 🙂 Jim PS. Jalview uses a similar mechanism to get the attributes imported as features on associated sequences. ________________________________ From: Javier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: 12 March 2025 08:42 To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Obtain individual RMSD values Hello, I have an issue when applying matchmaker command in ChimeraX. When I execute the command: matchmaker #1 to #2 showAlignment true I obtain the alignment with the bars in the upper layer showing the individual RMSD of each residue. But the results yields the overall RMSD of the alignment (i.e. RMSD between 108 pruned atoms). Is there any way to obtain those individual RMSDs of the alignment as a file or have them printed in the log for post-processing? Thank you in advance _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.ucsf.edu%2Fmailman%2Farchives%2Flist%2Fchimerax-users%40cgl.ucsf.edu%2F&data=05%7C02%7CJ.Procter%40dundee.ac.uk%7Ca6c2fb9e552e4dd7dc5808dd61423031%7Cae323139093a4d2a81a65d334bcd9019%7C0%7C0%7C638773659117915708%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=sAc4o5vk8pGms%2BZPuGwAjnNehmnUs9EQF5TQp9LVYwA%3D&reserved=0<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> The University of Dundee is a registered Scottish Charity, No: SC015096